April 26-May 9, 2006

YT wants to apologize for is a rushed and late ListSummaries report this week; he’s getting a poster together and heading off to a conference. Speaking of conference, the next ListSummaries report will not be posted until May 26. It would have been on time that week but YT’s better half had a laptop malfunction and Steve Job’s and Co. decided not to release the newest MacBooks until mid-May. Sigh…

I am making a small change this week; I’m adding ‘’Announcements’’ to the top of the list. These are anything, well, announced to the world at large (releases, changes in code, etc.).

Make sure to show the ‘orphans’ your love! Well, except YT and his mad ramblings…

Paul Mooney makes a change to Bio::DB::GFF for parsing all the special tags for GFF3. YT, being skittish from all the commits coming from the GMOD guys, warns that they probably need to make change. Scott Cain, paying rapt attention, obliges…

Problems with parsing bacterial strain from EMBL OS or RC lines

Mark A. Miller notes problems with parsing the strain information from bacterial species. Jason and Brian O. point out the previous thread talking about this, and James Abbott adds that his $job is keeping him busy at the moment but has it on his priority list.

Marco Blanchette reveals a possible problem with Bio::DB::GFF when using the intersection function from a Bio::RangeI object. Malcolm Cook and Sean Davis offer suggestions. Marco digresses on a tangent about how to get the BioPerl version number, which Heikki and Torsten gladly share…

Problems in GenBank CONTIG parsing

Michael Rogoff points out a serious bug in GenBank file parsing when there is a CONTIG line present. YT decides to make a bug fix to Bio::SeqIO::genbank to get around this issue and crosses his fingers that it doesn’t break anything. He also makes related changes to Bio::DB::NCBIHelper to allow direct downloading these GenBank CON files (see below)…

Frames, strands, and BLASTX

T.D. Houfek points out that using Bio::Seq::Quality to write FASTA-style quality files doesn’t output the expected description line. Hilmar offers a suggestion to check it out but Dave Messina provides a fix…

Problems with BLAST file parsing

Hubert Prielinger submitted a problem with parsing multiple BLAST reports. After various attempts, a bug submission, and some ‘hemming and hawing’, Jason finally points out that the logic of the loop was in error…

AlignIO problems parsing FASTA files

Jason responds to an off-list email about problems with parsing FASTA files using Bio::AlignIO. Turns out there was an errant space causing the problem. He then realizes that Gloria may be just trying to read sequences so suggests using Bio::SeqIO and using the HOWTO’s…

Primer Parameters and Primer3 Parsing, post haste

Chen Li wanted to know how to change a parameter for Bio::Tools::Run::Primer3 to increase the PCR product size. Various suggestions were put forward, with Roy Chaudhuri providing the final solution. Chen then submitted a second issue, in which results were being overwritten; Brian O. and Paul Wiersma offer solutions, including using Bio::Tools::Primer3…

Bioperl-guts (for the die-hards)

Note: Significant module changes and additions to CVS are normally announced on the main bioperl-l list if they are in decent enough condition for production work. If modules listed below have not been announced, then there may be a very good reason for it. If you plan on trying to use these, consider contacting the author(s). Many of the modules discussed in this section are highly experimental and are in various stages of development. They may or may not work at all. Therefore, we are not responsible for any problems faced with using this code.

NEW - Bug 1986 - SearchIO::blast mixes up hits where duplicate accessions are present. Not sure what to think about this bug; is a database that has accessions with exactly the same name considered legitimate? YT and Jason take this one on…

NEW – RESOLVED - Bug 1988 - SearchIO::blast parses bit score incorrectly when score is reported in scientific notation – looks like this was fixed in CVS a while ago.

NEW - Bug 1993 - Changes to Bio:::SeqIO::genbank – YT announces change to the way the CONTIG line is parsed in GenBank CON files; this is a placeholder bug in case someone wonders why their script broke due to this change